diff --git a/microfilm/dataset/dataset.py b/microfilm/dataset/dataset.py index 8a09fc1..72b631f 100644 --- a/microfilm/dataset/dataset.py +++ b/microfilm/dataset/dataset.py @@ -229,7 +229,8 @@ def __init__( def initialize(self): - from aicsimageio import AICSImage, readers + from bioio import BioImage + import bioio_tifffile # if no channel names are provided, consider all folders as channel if self.channel_name is None: @@ -240,7 +241,7 @@ def initialize(self): self.channelfile = self.channel_name self.channel_imobj = [ - AICSImage(os.path.join(self.expdir, x), dim_order="TYX", reader=readers.TiffReader) + BioImage(os.path.join(self.expdir, x), dim_order="TYX", reader=bioio_tifffile.Reader) for x in self.channel_name ] diff --git a/setup.cfg b/setup.cfg index d4812fd..de2f5f6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -44,14 +44,16 @@ install_requires = [options.extras_require] multipage = - aicsimageio + bioio + bioio-tifffile nd2 = nd2reader animation = imageio-ffmpeg ipywidgets all = - aicsimageio + bioio + bioio-tifffile nd2reader imageio-ffmpeg ipywidgets